1W77

2C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.349 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.237 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

The Crystal Structure of a Plant 2C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase Exhibits a Distinct Quaternary Structure Compared to Bacterial Homologues and a Possible Role in Feedback Regulation for Cytidine Monophosphate.

Gabrielsen, M.Kaiser, J.Rohdich, F.Eisenreich, W.Laupitz, R.Bacher, A.Bond, C.S.Hunter, W.N.

(2006) FEBS J 273: 1065

  • DOI: https://doi.org/10.1111/j.1742-4658.2006.05133.x
  • Primary Citation of Related Structures:  
    1W77

  • PubMed Abstract: 

    The homodimeric 2C-methyl-D-erythritol 4-phosphate cytidylyltransferase contributes to the nonmevalonate pathway of isoprenoid biosynthesis. The crystal structure of the catalytic domain of the recombinant enzyme derived from the plant Arabidopsis thaliana has been solved by molecular replacement and refined to 2.0 A resolution. The structure contains cytidine monophosphate bound in the active site, a ligand that has been acquired from the bacterial expression system, and this observation suggests a mechanism for feedback regulation of enzyme activity. Comparisons with bacterial enzyme structures, in particular the enzyme from Escherichia coli, indicate that whilst individual subunits overlay well, the arrangement of subunits in each functional dimer is different. That distinct quaternary structures are available, in conjunction with the observation that the protein structure contains localized areas of disorder, suggests that conformational flexibility may contribute to the function of this enzyme.


  • Organizational Affiliation

    Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE228Arabidopsis thalianaMutation(s): 1 
EC: 2.7.7.60
UniProt
Find proteins for P69834 (Arabidopsis thaliana)
Explore P69834 
Go to UniProtKB:  P69834
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69834
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.349 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.237 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.496α = 90
b = 74.496β = 90
c = 223.026γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
BEASTphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-21
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description